1
|
Qian G, Zhang H, Liu Y, Shribak M, Eliceiri KW, Provenzano PP. Computationally enabled polychromatic polarized imaging enables mapping of matrix architectures that promote pancreatic ductal adenocarcinoma dissemination. THE AMERICAN JOURNAL OF PATHOLOGY 2025:S0002-9440(25)00160-9. [PMID: 40350060 DOI: 10.1016/j.ajpath.2025.04.017] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/18/2024] [Revised: 02/22/2025] [Accepted: 04/08/2025] [Indexed: 05/14/2025]
Abstract
Pancreatic ductal adenocarcinoma (PDA) is an extremely metastatic and lethal disease. In PDA, extracellular matrix (ECM) architectures known as Tumor-Associated Collagen Signatures (TACS) regulate invasion and metastatic spread in both early dissemination and in late-stage disease. As such, TACS has been suggested as a biomarker to aid in pathologic assessment. However, despite its significance, approaches to quantitatively capture these ECM patterns currently require advanced optical systems with signaling processing analysis. Here we present an expansion of polychromatic polarized microscopy (PPM) with inherent angular information coupled to machine learning and computational pixel-wise analysis of TACS. Using this platform, we are able to accurately capture TACS architectures in H&E stained histology sections directly through PPM contrast. Moreover, PPM facilitated identification of transitions to dissemination architectures, i.e., transitions from sequestration through expansion to dissemination from both PanINs and throughout PDA. Lastly, PPM evaluation of architectures in liver metastases, the most common metastatic site for PDA, demonstrates TACS-mediated focal and local invasion as well as identification of unique patterns anchoring aligned fibers into normal-adjacent tumor, suggesting that these patterns may be precursors to metastasis expansion and local spread from micrometastatic lesions. Combined, these findings demonstrate that PPM coupled to computational platforms is a powerful tool for analyzing ECM architecture that can be employed to advance cancer microenvironment studies and provide clinically relevant diagnostic information.
Collapse
Affiliation(s)
- Guhan Qian
- Department of Biomedical Engineering, University of Minnesota; Center for Multiparametric Imaging of Tumor Immune Microenvironments, University of Minnesota and University of Wisconsin-Madison
| | - Hongrong Zhang
- Department of Biomedical Engineering, University of Minnesota; Center for Multiparametric Imaging of Tumor Immune Microenvironments, University of Minnesota and University of Wisconsin-Madison
| | - Yuming Liu
- Center for Multiparametric Imaging of Tumor Immune Microenvironments, University of Minnesota and University of Wisconsin-Madison; Center for Quantitative Cell Imaging, University of Wisconsin-Madison, Madison, WI
| | - Michael Shribak
- Marine Biological Laboratory, University of Chicago, Woods Hole, MA
| | - Kevin W Eliceiri
- Center for Multiparametric Imaging of Tumor Immune Microenvironments, University of Minnesota and University of Wisconsin-Madison; Center for Quantitative Cell Imaging, University of Wisconsin-Madison, Madison, WI; Department of Medical Physics, University of Wisconsin-Madison, Madison, WI
| | - Paolo P Provenzano
- Department of Biomedical Engineering, University of Minnesota; Center for Multiparametric Imaging of Tumor Immune Microenvironments, University of Minnesota and University of Wisconsin-Madison; Masonic Cancer Center, University of Minnesota; Dept of Medicine, Div. of Hematology, Oncology, and Transplantation, University of Minnesota; Institute for Engineering in Medicine, University of Minnesota; Stem Cell Institute, University of Minnesota.
| |
Collapse
|
2
|
Chitsaz M, Yang L, Rayes-Danan R, Savari O, Li B, Shribak M, Eliceiri K, Loeffler A. Polychromatic Polarization Microscopy Differentiates Collagen Fiber Signatures in Benign Pancreatic Tissue and Pancreatic Ductal Adenocarcinoma. Mod Pathol 2025; 38:100768. [PMID: 40210130 DOI: 10.1016/j.modpat.2025.100768] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2024] [Revised: 03/20/2025] [Accepted: 03/30/2025] [Indexed: 04/12/2025]
Abstract
The orientation of collagen fibers in relation to malignant epithelium is known to carry prognostic information in a variety of tissues. The data are the strongest for breast and pancreatic ductal adenocarcinoma. However, information inherent in collagen fiber topology in malignant tissues remains untapped in daily surgical pathology practice, largely because collagen fibers within areas of desmoplasia cannot be resolved with standard diagnostic microscopy. The methodologies used to visualize collagen fiber orientation are either of insufficient resolution to consistently capture collagen fiber topology or require resources in time and money that do not fit into the daily surgical pathology workflow. Polychromatic polarization microscopy has the potential to bring collagen topology to the attention of pathologists during their routine work. It has been demonstrated to be equivalent to the gold standard methodology used to research collagen, second harmonic generation. We use polychromatic polarization microscopy to visualize and describe the differences in collagen topology in normal pancreas, chronic pancreatitis, and pancreatic ductal adenocarcinoma with a standard microscope, using hematoxylin and eosin-stained sections. In the process, we propose a lexicon with which to describe the morphologic characteristics of collagen in benign and malignant pancreatic tissues.
Collapse
Affiliation(s)
- Mahsa Chitsaz
- Department of Pathology, Cleveland Clinic Foundation, Cleveland, Ohio
| | - Linlin Yang
- Department of Pathology, Cleveland Clinic Foundation, Cleveland, Ohio
| | - Rania Rayes-Danan
- Department of Pathology, MetroHealth Medical Center, Cleveland, Ohio
| | - Omid Savari
- Department of Pathology, University Hospitals Cleveland Medical Center, Cleveland, Ohio
| | - Bin Li
- Department of Engineering Science, University of Oxford, Oxford, United Kingdom
| | | | - Kevin Eliceiri
- Center for Quantitative Cell Imaging, University of Wisconsin, Madison, Wisconsin; Morgridge Institute for Research, Madison, Wisconsin
| | - Agnes Loeffler
- Department of Pathology, MetroHealth Medical Center, Cleveland, Ohio.
| |
Collapse
|
3
|
Martens K, de Almeida NM, Shribak M, Higuti J, Schön I. On Cytheridellawhitmani sp. nov. (Crustacea, Ostracoda) from Cape Cod (Massachusetts, USA), with a reappraisal of the taxonomy of the genus. Zookeys 2025; 1224:317-348. [PMID: 39935609 PMCID: PMC11811716 DOI: 10.3897/zookeys.1224.135458] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2024] [Accepted: 12/04/2024] [Indexed: 02/13/2025] Open
Abstract
Cytheridellawhitmani Martens, sp. nov. is described from lakes on Cape Cod (MA, USA). The species differs from its congeners mainly by the shape of the female carapace and by the morphology of the hemipenis, especially of the distal lobe and the copulatory process. The literature on the genus is reviewed and the synonymy of the fossil Cytheridellaboldii Purper, 1974 with the type species C.ilosvayi Daday, 1905, both described from South America, is confirmed. The status of Cytheridellaamericana (Furtos, 1936) is reverted to that of "uncertain species". Beside the type species and the new species, the genus currently includes only three further species from Africa: C.monodi Klie, 1936, C.damasi Klie, 1944 (with synonym C.chariessa Rome, 1977), and C.tepida Victor, 1987. The morphology of the new species is discussed in comparison with the congeneric species, especially regarding the valve ornamentation, the structure and function of the third thoracopod, the hemipenis and the caudal ramus. It is suggested that C.whitmani is a recent invasive species in the lakes of the Cape Cod peninsula. Its occurrence at northern latitudes is unexpected, as its congeneric species are consistently (sub-) tropical.
Collapse
Affiliation(s)
- Koen Martens
- Royal Belgian Institute of Natural Sciences, Freshwater Biology, Vautierstraat 29, B-1000 Brussels, Belgium
- Department of Biology, Ghent University, K.L. Ledeganckstraat 35, B-9000 Ghent, Belgium
| | - Nadiny Martins de Almeida
- Royal Belgian Institute of Natural Sciences, Freshwater Biology, Vautierstraat 29, B-1000 Brussels, Belgium
- Graduate Program in Ecology of Inland Water Ecosystems (PEA), Department of Biology (DBI), Centre of Biological Sciences (CCB), State University of Maringá (UEM), Av. Colombo, 5790, CEP 87020-900, Maringá, PR, Brazil
| | | | - Janet Higuti
- Graduate Program in Ecology of Inland Water Ecosystems (PEA), Department of Biology (DBI), Centre of Biological Sciences (CCB), State University of Maringá (UEM), Av. Colombo, 5790, CEP 87020-900, Maringá, PR, Brazil
| | - Isa Schön
- Royal Belgian Institute of Natural Sciences, Freshwater Biology, Vautierstraat 29, B-1000 Brussels, Belgium
- Centre of Research in Limnology, Ichthyology and Aquaculture (Nupélia), Centre of Biological Sciences (CCB), State University of Maringá (UEM), Av. Colombo, 5790, CEP 87020-900. Maringá, PR, Brazil
| |
Collapse
|
4
|
Guizetti J. Imaging malaria parasites across scales and time. J Microsc 2025. [PMID: 39749880 DOI: 10.1111/jmi.13384] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2024] [Revised: 12/13/2024] [Accepted: 12/23/2024] [Indexed: 01/04/2025]
Abstract
The idea that disease is caused at the cellular level is so fundamental to us that we might forget the critical role microscopy played in generating and developing this insight. Visually identifying diseased or infected cells lays the foundation for any effort to curb human pathology. Since the discovery of the Plasmodium-infected red blood cells, which cause malaria, microscopy has undergone an impressive development now literally resolving individual molecules. This review explores the expansive field of light microscopy, focusing on its application to malaria research. Imaging technologies have transformed our understanding of biological systems, yet navigating the complex and ever-growing landscape of techniques can be daunting. This review offers a guide for researchers, especially those working on malaria, by providing historical context as well as practical advice on selecting the right imaging approach. The review advocates an integrated methodology that prioritises the research question while considering key factors like sample preparation, fluorophore choice, imaging modality, and data analysis. In addition to presenting seminal studies and innovative applications of microscopy, the review highlights a broad range of topics, from traditional techniques like white light microscopy to advanced methods such as superresolution microscopy and time-lapse imaging. It addresses the emerging challenges of microscopy, including phototoxicity and trade-offs in resolution and speed, and offers insights into future technologies that might impact malaria research. This review offers a mix of historical perspective, technological progress, and practical guidance that appeal to novice and advanced microscopists alike. It aims to inspire malaria researchers to explore imaging techniques that could enrich their studies, thus advancing the field through enhanced visual exploration of the parasite across scales and time.
Collapse
Affiliation(s)
- Julien Guizetti
- Centre for Infectious Diseases, Heidelberg University Hospital, Heidelberg, Germany
| |
Collapse
|
5
|
Acevedo Zamora MA, Schrank CE, Kamber BS. Using the traditional microscope for mineral grain orientation determination: A prototype image analysis pipeline for optic-axis mapping (POAM). J Microsc 2024; 295:147-176. [PMID: 38441305 DOI: 10.1111/jmi.13284] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2023] [Revised: 02/09/2024] [Accepted: 02/16/2024] [Indexed: 07/13/2024]
Abstract
This paper reports on the development of an open-source image analysis software 'pipeline' dedicated to petrographic microscopy. Using conventional rock thin sections and images from a standard polarising microscope, the pipeline can classify minerals and subgrains into objects and obtain information about optic-axis orientation. Five metamorphic rocks were chosen to test and illustrate the method. Thin sections were imaged using reflected and cross- and plane-polarised transmitted light. Images were taken at different angles of the polariser and analyser (360° with 10° steps), both with and without the full-lambda plate. The resulting image stacks were analysed with a modular pipeline for optic-axis mapping (POAM). POAM consists of external and internal software packages that register, segment, classify, and interpret the visible light spectra using object-based image analysis (OBIAS). The mapped fields-of-view and grain orientation stereonets of interest are presented in the context of whole-slide images. Two innovations are reported. First, we used hierarchical tree region merging on blended multimodal images to classify individual grains of rock-forming minerals into objects. Second, we assembled a new optical mineralogy algorithm chain that identifies the mineral slow axis orientation. The c-axis orientation results were verified with scanning electron microscopy electron backscattered diffraction (SEM-EBSD) data. For quartz (uniaxial) in a granite mylonite the test yielded excellent correspondence of c-axis azimuth and good agreement for inclination. For orthorhombic orthopyroxene in a deformed garnet harzburgite, POAM produced acceptable results for slow axis azimuth. In addition, the method identified slight anisotropy in garnet that would not be appreciated by traditional microscopy. We propose that our method is ideally suited for two commonly performed tasks in mineralogy. First, for mineral grain classification of entire thin sections scans on blended images to provide automated modal abundance estimates and grain size distribution. Second, for prospective fields of view of interest, POAM can rapidly generate slow axis crystal orientation maps from multiangle image stacks on conventionally prepared thin sections for targeting detailed SEM-EBSD studies.
Collapse
Affiliation(s)
- Marco Andres Acevedo Zamora
- School of Earth and Atmospheric Sciences, Queensland University of Technology, Brisbane, Queensland, Australia
| | - Christoph Eckart Schrank
- School of Earth and Atmospheric Sciences, Queensland University of Technology, Brisbane, Queensland, Australia
| | - Balz Samuel Kamber
- School of Earth and Atmospheric Sciences, Queensland University of Technology, Brisbane, Queensland, Australia
| |
Collapse
|
6
|
Ji F, Islam MR, Wang B, Hua Y, Sigal IA. Lamina Cribrosa Insertions Into the Sclera Are Sparser, Narrower, and More Slanted in the Anterior Lamina. Invest Ophthalmol Vis Sci 2024; 65:35. [PMID: 38648038 PMCID: PMC11044832 DOI: 10.1167/iovs.65.4.35] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2023] [Accepted: 04/03/2024] [Indexed: 04/25/2024] Open
Abstract
Purpose The lamina cribrosa (LC) depends on the sclera for support. The support must be provided through the LC insertions. Although a continuous insertion over the whole LC periphery is often assumed, LC insertions are actually discrete locations where LC collagenous beams meet the sclera. We hypothesized that LC insertions vary in number, size, and shape by quadrant and depth. Methods Coronal cryosections through the full LCs from six healthy monkey eyes were imaged using instant polarized light microscopy. The images were registered into a stack, on which we manually marked LC insertion outlines, nothing their position in-depth and quadrant (inferior, superior, nasal, or temporal). From the marks, we determined the insertion number, width, angle to the canal wall (90 degrees = perpendicular), and insertion ratio (fraction of LC periphery represented by insertions). Using linear mixed effect models, we determined if the insertion characteristics were associated with depth or quadrant. Results Insertions in the anterior LC were sparser, narrower, and more slanted than those in deeper LC (P values < 0.001). There were more insertions spanning a larger ratio of the canal wall in the middle LC than in the anterior and posterior (P values < 0.001). In the nasal quadrant, the insertion angles were significantly smaller (P < 0.001). Conclusions LC insertions vary substantially and significantly over the canal. The sparser, narrower, and more slanted insertions of the anterior-most LC may not provide the robust support afforded by insertions of the middle and posterior LC. These variations may contribute to the progressive deepening of the LC and regional susceptibility to glaucoma.
Collapse
Affiliation(s)
- Fengting Ji
- Department of Ophthalmology, University of Pittsburgh, Pittsburgh, Pennsylvania, United States
- Department of Bioengineering, University of Pittsburgh, Pittsburgh, Pennsylvania, United States
| | - Mohammad R. Islam
- Department of Ophthalmology, University of Pittsburgh, Pittsburgh, Pennsylvania, United States
- Department of Mechanical Engineering, University of Texas Rio Grande Valley, Edinburg, Texas, United States
| | - Bingrui Wang
- Department of Ophthalmology, University of Pittsburgh, Pittsburgh, Pennsylvania, United States
| | - Yi Hua
- Department of Ophthalmology, University of Pittsburgh, Pittsburgh, Pennsylvania, United States
- Department of Biomedical Engineering, University of Mississippi, University, Mississippi, United States
| | - Ian A. Sigal
- Department of Ophthalmology, University of Pittsburgh, Pittsburgh, Pennsylvania, United States
- Department of Bioengineering, University of Pittsburgh, Pittsburgh, Pennsylvania, United States
| |
Collapse
|
7
|
Jum'ah H, Shribak M, Keikhosravi A, Li B, Liu Y, Obaidat D, Eliceiri KW, Loeffler A, Ayub S. Detection of crystals in joint fluid aspirates with polychromatic polarisation microscopy. Ann Rheum Dis 2023; 82:1501-1502. [PMID: 37236769 PMCID: PMC10592475 DOI: 10.1136/ard-2023-224331] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2023] [Accepted: 05/15/2023] [Indexed: 05/28/2023]
Affiliation(s)
- Husam Jum'ah
- Department of Pathology, MetroHealth Medical Center, Cleveland, Ohio, USA
| | - Michael Shribak
- Marine Biological Laboratory, University of Chicago, Woods Hole, Massachusetts, USA
| | - Adib Keikhosravi
- National Cancer Institute, National Institutes of Health, Bethesda, Maryland, USA
- Laboratory for Optical and Computational Instrumentation, University of Wisconsin-Madison, Madison, Wisconsin, USA
| | - Bin Li
- Laboratory for Optical and Computational Instrumentation, University of Wisconsin-Madison, Madison, Wisconsin, USA
- Morgridge Institute for Research, Madison, Wisconsin, USA
| | - Yuming Liu
- Laboratory for Optical and Computational Instrumentation, University of Wisconsin-Madison, Madison, Wisconsin, USA
| | - Deya Obaidat
- Department of Rheumatology, Parkview Health, Fort Wayne, Indiana, USA
| | - Kevin W Eliceiri
- Laboratory for Optical and Computational Instrumentation, University of Wisconsin-Madison, Madison, Wisconsin, USA
- Morgridge Institute for Research, Madison, Wisconsin, USA
- Department of Medical Physics, University of Wisconsin-Madison, Madison, Wisconsin, USA
| | - Agnes Loeffler
- Department of Pathology, MetroHealth Medical Center, Cleveland, Ohio, USA
| | - Salman Ayub
- Department of Pathology, MetroHealth Medical Center, Cleveland, Ohio, USA
| |
Collapse
|
8
|
Bessif B, Heck B, Pfohl T, Le CMQ, Chemtob A, Pirela V, Elgoyhen J, Tomovska R, Müller AJ, Reiter G. Nucleation Assisted through the Memory of a Polymer Melt: A Different Polymorph Emerging from the Melt of Another One. Macromolecules 2023. [DOI: 10.1021/acs.macromol.2c02252] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/17/2023]
Affiliation(s)
- Brahim Bessif
- Institute of Physics, University of Freiburg, Hermann-Herder-Straße 3, Freiburg 79104, Germany
| | - Barbara Heck
- Institute of Physics, University of Freiburg, Hermann-Herder-Straße 3, Freiburg 79104, Germany
| | - Thomas Pfohl
- Institute of Physics, University of Freiburg, Hermann-Herder-Straße 3, Freiburg 79104, Germany
| | - Cuong Minh Quoc Le
- Institut de Sciences des Matériaux de Mulhouse (IS2M), UMR CNRS 7361, Université de Haute-Alsace, 15 Rue Jean Starcky, Mulhouse, Cedex 68057, France
| | - Abraham Chemtob
- Institut de Sciences des Matériaux de Mulhouse (IS2M), UMR CNRS 7361, Université de Haute-Alsace, 15 Rue Jean Starcky, Mulhouse, Cedex 68057, France
| | - Valentina Pirela
- Polymat and Department of Polymers and Advanced Materials: Physics, Chemistry and Technology, Faculty of Chemistry, University of the Basque Country UPV/EHU, Paseo Manuel de Lardizabal 3, 20018 Donostia-San Sebastián, Spain
| | - Justine Elgoyhen
- Polymat and Department of Polymers and Advanced Materials: Physics, Chemistry and Technology, Faculty of Chemistry, University of the Basque Country UPV/EHU, Paseo Manuel de Lardizabal 3, 20018 Donostia-San Sebastián, Spain
| | - Radmila Tomovska
- Polymat and Department of Polymers and Advanced Materials: Physics, Chemistry and Technology, Faculty of Chemistry, University of the Basque Country UPV/EHU, Paseo Manuel de Lardizabal 3, 20018 Donostia-San Sebastián, Spain
- IKERBASQUE, Basque Foundation for Science, Plaza Euskadi 5, 48009 Bilbao, Spain
| | - Alejandro J. Müller
- Polymat and Department of Polymers and Advanced Materials: Physics, Chemistry and Technology, Faculty of Chemistry, University of the Basque Country UPV/EHU, Paseo Manuel de Lardizabal 3, 20018 Donostia-San Sebastián, Spain
- IKERBASQUE, Basque Foundation for Science, Plaza Euskadi 5, 48009 Bilbao, Spain
| | - Günter Reiter
- Institute of Physics, University of Freiburg, Hermann-Herder-Straße 3, Freiburg 79104, Germany
- IKERBASQUE, Basque Foundation for Science, Plaza Euskadi 5, 48009 Bilbao, Spain
| |
Collapse
|
9
|
Hugonnet H, Shin S, Park Y. Regularization of dielectric tensor tomography. OPTICS EXPRESS 2023; 31:3774-3783. [PMID: 36785362 DOI: 10.1364/oe.478260] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/14/2022] [Accepted: 01/02/2023] [Indexed: 06/18/2023]
Abstract
Dielectric tensor tomography reconstructs the three-dimensional dielectric tensors of microscopic objects and provides information about the crystalline structure orientations and principal refractive indices. Because dielectric tensor tomography is based on transmission measurement, it suffers from the missing cone problem, which causes poor axial resolution, underestimation of the refractive index, and halo artifacts. In this study, we study the application of total variation and positive semi-definiteness regularization to three-dimensional tensor distributions. In particular, we demonstrate the reduction of artifacts when applied to dielectric tensor tomography.
Collapse
|
10
|
Nelson MS, Liu Y, Wilson HM, Li B, Rosado-Mendez IM, Rogers JD, Block WF, Eliceiri KW. Multiscale Label-Free Imaging of Fibrillar Collagen in the Tumor Microenvironment. Methods Mol Biol 2023; 2614:187-235. [PMID: 36587127 DOI: 10.1007/978-1-0716-2914-7_13] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
With recent advances in cancer therapeutics, there is a great need for improved imaging methods for characterizing cancer onset and progression in a quantitative and actionable way. Collagen, the most abundant extracellular matrix protein in the tumor microenvironment (and the body in general), plays a multifaceted role, both hindering and promoting cancer invasion and progression. Collagen deposition can defend the tumor with immunosuppressive effects, while aligned collagen fiber structures can enable tumor cell migration, aiding invasion and metastasis. Given the complex role of collagen fiber organization and topology, imaging has been a tool of choice to characterize these changes on multiple spatial scales, from the organ and tumor scale to cellular and subcellular level. Macroscale density already aids in the detection and diagnosis of solid cancers, but progress is being made to integrate finer microscale features into the process. Here we review imaging modalities ranging from optical methods of second harmonic generation (SHG), polarized light microscopy (PLM), and optical coherence tomography (OCT) to the medical imaging approaches of ultrasound and magnetic resonance imaging (MRI). These methods have enabled scientists and clinicians to better understand the impact collagen structure has on the tumor environment, at both the bulk scale (density) and microscale (fibrillar structure) levels. We focus on imaging methods with the potential to both examine the collagen structure in as natural a state as possible and still be clinically amenable, with an emphasis on label-free strategies, exploiting intrinsic optical properties of collagen fibers.
Collapse
Affiliation(s)
- Michael S Nelson
- Center for Quantitative Cell Imaging, University of Wisconsin-Madison, Madison, WI, USA.,Department of Biomedical Engineering, University of Wisconsin-Madison, Madison, WI, USA
| | - Yuming Liu
- Center for Quantitative Cell Imaging, University of Wisconsin-Madison, Madison, WI, USA
| | - Helen M Wilson
- Center for Quantitative Cell Imaging, University of Wisconsin-Madison, Madison, WI, USA.,Department of Biomedical Engineering, University of Wisconsin-Madison, Madison, WI, USA
| | - Bin Li
- Center for Quantitative Cell Imaging, University of Wisconsin-Madison, Madison, WI, USA.,Department of Biomedical Engineering, University of Wisconsin-Madison, Madison, WI, USA.,Morgridge Institute for Research, Madison, WI, USA
| | - Ivan M Rosado-Mendez
- Department of Medical Physics, University of Wisconsin-Madison, Madison, WI, USA
| | - Jeremy D Rogers
- Morgridge Institute for Research, Madison, WI, USA.,McPherson Eye Research Institute, University of Wisconsin-Madison, Madison, WI, USA
| | - Walter F Block
- Department of Medical Physics, University of Wisconsin-Madison, Madison, WI, USA
| | - Kevin W Eliceiri
- Center for Quantitative Cell Imaging, University of Wisconsin-Madison, Madison, WI, USA. .,Department of Biomedical Engineering, University of Wisconsin-Madison, Madison, WI, USA. .,Morgridge Institute for Research, Madison, WI, USA. .,Department of Medical Physics, University of Wisconsin-Madison, Madison, WI, USA. .,McPherson Eye Research Institute, University of Wisconsin-Madison, Madison, WI, USA.
| |
Collapse
|
11
|
Chavda VP, Dawre S, Pandya A, Vora LK, Modh DH, Shah V, Dave DJ, Patravale V. Lyotropic liquid crystals for parenteral drug delivery. J Control Release 2022; 349:533-549. [PMID: 35792188 DOI: 10.1016/j.jconrel.2022.06.062] [Citation(s) in RCA: 32] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2022] [Revised: 06/27/2022] [Accepted: 06/29/2022] [Indexed: 10/17/2022]
Abstract
The necessity for long-term treatments of chronic diseases has encouraged the development of novel long-acting parenteral formulations intending to improve drug pharmacokinetics and therapeutic efficacy. Lately, one of the novel approaches has been developed based on lipid-based liquid crystals. The lyotropic liquid crystal (LLC) systems consist of amphiphilic molecules and are formed in presence of solvents with the most common types being cubic, hexagonal and lamellar mesophases. LC injectables have been recently developed based on polar lipids that spontaneously form liquid crystal nanoparticles in aqueous tissue environments to create the in-situ long-acting sustained-release depot to provide treatment efficacy over extended periods. In this manuscript, we have consolidated and summarized the various type of liquid crystals, recent formulation advancements, analytical evaluation, and therapeutic application of lyotropic liquid crystals in the field of parenteral sustained release drug delivery.
Collapse
Affiliation(s)
- Vivek P Chavda
- Department of Pharmaceutics and Pharmaceutical Technology, L M College of Pharmacy, Ahmedabad 380009, India; Department of Pharmaceutics & Pharm, Technology, K. B. Institute of Pharmaceutical Education and Research, Kadi Sarva Vishwavidyalaya, Gandhinagar 382023, Gujarat, India.
| | - Shilpa Dawre
- Department of Pharmaceutics, SVKM's Narsee Monjee Institute of Management Studies (NMIMS), Shirpur, India
| | - Anjali Pandya
- Department of Pharmaceutical Sciences and Technology, Institute of Chemical Technology, Mumbai 400 019, India
| | - Lalitkumar K Vora
- School of Pharmacy, Queen's University Belfast, 97 Lisburn Road, BT9 7BL, UK.
| | - Dharti H Modh
- Department of Medicinal Chemistry, Bharati Vidyapeeth's Poona College of Pharmacy, Pune, India
| | - Vidhi Shah
- Department of Pharmaceutics and Pharmaceutical Technology, L M College of Pharmacy, Ahmedabad 380009, India
| | - Divyang J Dave
- Department of Pharmaceutics & Pharm, Technology, K. B. Institute of Pharmaceutical Education and Research, Kadi Sarva Vishwavidyalaya, Gandhinagar 382023, Gujarat, India
| | - Vandana Patravale
- Department of Pharmaceutical Sciences and Technology, Institute of Chemical Technology, Mumbai 400 019, India
| |
Collapse
|
12
|
Laurinavicius A, Rasmusson A, Plancoulaine B, Shribak M, Levenson R. Machine-Learning-Based Evaluation of Intratumoral Heterogeneity and Tumor-Stroma Interface for Clinical Guidance. THE AMERICAN JOURNAL OF PATHOLOGY 2021; 191:1724-1731. [PMID: 33895120 PMCID: PMC11727842 DOI: 10.1016/j.ajpath.2021.04.008] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/16/2021] [Accepted: 04/15/2021] [Indexed: 12/21/2022]
Abstract
Assessment of intratumoral heterogeneity and tumor-host interaction within the tumor microenvironment is becoming increasingly important for innovative cancer therapy decisions because of the unique information it can generate about the state of the disease. However, its assessment and quantification are limited by ambiguous definitions of the tumor-host interface and by human cognitive capacity in current pathology practice. Advances in machine learning and artificial intelligence have opened the field of digital pathology to novel tissue image analytics and feature extraction for generation of high-capacity computational disease management models. A particular benefit is expected from machine-learning applications that can perform extraction and quantification of subvisual features of both intratumoral heterogeneity and tumor microenvironment aspects. These methods generate information about cancer cell subpopulation heterogeneity, potential tumor-host interactions, and tissue microarchitecture, derived from morphologically resolved content using both explicit and implicit features. Several studies have achieved promising diagnostic, prognostic, and predictive artificial intelligence models that often outperform current clinical and pathology criteria. However, further effort is needed for clinical adoption of such methods through development of standardizable high-capacity workflows and proper validation studies.
Collapse
Affiliation(s)
- Arvydas Laurinavicius
- Department of Pathology, Forensic Medicine and Pharmacology, Institute of Biomedical Sciences of the Faculty of Medicine of Vilnius University, Vilnius, Lithuania; National Center of Pathology, Affiliate of Vilnius University Hospital Santaros Klinikos, Vilnius, Lithuania.
| | - Allan Rasmusson
- Department of Pathology, Forensic Medicine and Pharmacology, Institute of Biomedical Sciences of the Faculty of Medicine of Vilnius University, Vilnius, Lithuania; National Center of Pathology, Affiliate of Vilnius University Hospital Santaros Klinikos, Vilnius, Lithuania
| | - Benoit Plancoulaine
- Department of Pathology, Forensic Medicine and Pharmacology, Institute of Biomedical Sciences of the Faculty of Medicine of Vilnius University, Vilnius, Lithuania; ANTICIPE, Inserm (UMR 1086), Cancer Center F. Baclesse, Normandy University, Caen, France
| | - Michael Shribak
- Department of Pathology, Forensic Medicine and Pharmacology, Institute of Biomedical Sciences of the Faculty of Medicine of Vilnius University, Vilnius, Lithuania; Marine Biological Laboratory of University of Chicago, Woods Hole, Massachusetts
| | - Richard Levenson
- Department of Pathology, Forensic Medicine and Pharmacology, Institute of Biomedical Sciences of the Faculty of Medicine of Vilnius University, Vilnius, Lithuania; Department of Pathology and Laboratory Medicine, University of California Davis Health, Sacramento, California
| |
Collapse
|
13
|
Keikhosravi A, Shribak M, Conklin MW, Liu Y, Li B, Loeffler A, Levenson RM, Eliceiri KW. Real-time polarization microscopy of fibrillar collagen in histopathology. Sci Rep 2021; 11:19063. [PMID: 34561546 PMCID: PMC8463693 DOI: 10.1038/s41598-021-98600-w] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2021] [Accepted: 08/31/2021] [Indexed: 12/20/2022] Open
Abstract
Over the past two decades, fibrillar collagen reorganization parameters such as the amount of collagen deposition, fiber angle and alignment have been widely explored in numerous studies. These parameters are now widely accepted as stromal biomarkers and linked to disease progression and survival time in several cancer types. Despite all these advances, there has not been a significant effort to make it possible for clinicians to explore these biomarkers without adding steps to the clinical workflow or by requiring high-cost imaging systems. In this paper, we evaluate previously described polychromatic polarization microscope (PPM) to visualize collagen fibers with an optically generated color representation of fiber orientation and alignment when inspecting the sample by a regular microscope with minor modifications. This system does not require stained slides, but is compatible with histological stains such as H&E. Consequently, it can be easily accommodated as part of regular pathology review of tissue slides, while providing clinically useful insight into stromal composition.
Collapse
Affiliation(s)
- Adib Keikhosravi
- Laboratory for Optical and Computational Instrumentation, Department of Biomedical Engineering, University of Wisconsin-Madison, Madison, WI, 53706, USA
| | - Michael Shribak
- Marine Biological Laboratory, University of Chicago, Woods Hole, MA, 02543, USA.
| | - Matthew W Conklin
- Deparment of Cell and Regenerative Biology, University of Wisconsin-Madison, Madison, WI, 53706, USA
| | - Yuming Liu
- Laboratory for Optical and Computational Instrumentation, Department of Biomedical Engineering, University of Wisconsin-Madison, Madison, WI, 53706, USA
| | - Bin Li
- Laboratory for Optical and Computational Instrumentation, Department of Biomedical Engineering, University of Wisconsin-Madison, Madison, WI, 53706, USA
- Morgridge Institute for Research, Madison, WI, 53715, USA
| | - Agnes Loeffler
- Department of Pathology, MetroHealth Medical Center, Cleveland, OH, 44109, USA
| | - Richard M Levenson
- Department of Pathology and Laboratory Medicine, UC Davis Health, Sacramento, CA, 95817, USA
| | - Kevin W Eliceiri
- Laboratory for Optical and Computational Instrumentation, Department of Biomedical Engineering, University of Wisconsin-Madison, Madison, WI, 53706, USA.
- Morgridge Institute for Research, Madison, WI, 53715, USA.
- Department of Medical Physics, University of Wisconsin-Madison, Madison, WI, 53705, USA.
| |
Collapse
|
14
|
Tumor collagen framework from bright-field histology images predicts overall survival of breast carcinoma patients. Sci Rep 2021; 11:15474. [PMID: 34326378 PMCID: PMC8322324 DOI: 10.1038/s41598-021-94862-6] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2021] [Accepted: 07/18/2021] [Indexed: 11/08/2022] Open
Abstract
Within the tumor microenvironment, specifically aligned collagen has been shown to stimulate tumor progression by directing the migration of metastatic cells along its structural framework. Tumor-associated collagen signatures (TACS) have been linked to breast cancer patient outcome. Robust and affordable methods for assessing biological information contained in collagen architecture need to be developed. We have developed a novel artificial neural network (ANN) based approach for tumor collagen segmentation from bright-field histology images and have tested it on a set of tissue microarray sections from early hormone receptor-positive invasive ductal breast carcinoma stained with Sirius Red (1 core per patient, n = 92). We designed and trained ANNs on sets of differently annotated image patches to segment collagen fibers and extracted 37 features of collagen fiber morphometry, density, orientation, texture, and fractal characteristics in the entire cohort. Independent instances of ANN models trained on highly differing annotations produced reasonably concordant collagen segmentation masks and allowed reliable prognostic Cox regression models (with likelihood ratios 14.11-22.99, at p-value < 0.05) superior to conventional clinical parameters (size of the primary tumor (T), regional lymph node status (N), histological grade (G), and patient age). Additionally, we noted statistically significant differences of collagen features between tumor grade groups, and the factor analysis revealed features resembling the TACS concept. Our proposed method offers collagen framework segmentation from bright-field histology images and provides novel image-based features for better breast cancer patient prognostication.
Collapse
|
15
|
Ramakrishnan S, Stagno JR, Magidson V, Heinz WF, Wang YX. Dependence of phase transition uniformity on crystal sizes characterized using birefringence. STRUCTURAL DYNAMICS (MELVILLE, N.Y.) 2021; 8:034301. [PMID: 34235229 PMCID: PMC8248999 DOI: 10.1063/4.0000098] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/02/2021] [Accepted: 04/29/2021] [Indexed: 06/13/2023]
Abstract
Solid-solid phase transitions (SSPTs) have been widely observed in crystals of organic or inorganic small-molecules. Although SSPTs in macromolecular crystals have been reported, the majority involve local atomic changes, such as those induced by changes in hydration. SSPTs driven by large conformational changes, however, can be more difficult to characterize since they often significantly disrupt lattice packing interactions. Such drastic changes make the cooperativity of molecular motion at the atomic level less easily achieved and more dependent on intrinsic properties of the crystal that define lattice order. Here, we investigate the effect of crystal size on the uniformity of SSPT in thin plate-like crystals of the adenine riboswitch aptamer RNA (riboA) by monitoring changes in crystal birefringence upon the diffusion of adenine ligand. The birefringence intensity is directly related to molecular order and the concurrent changes to polarizability of molecules that results from structural changes throughout the phase transition. The riboA crystals were loosely grouped into three categories (small, medium, and large) based on the surface area of the crystal plates. The time width of transition increased as a function of crystal size, ranging from ∼13 s for small crystals to ∼40 s for the largest crystal. Whereas the transitions in small crystals (<10 μm2) were mostly uniform throughout, the medium and large crystals exhibited large variations in the time and width of the transition peak depending on the region of the crystal being analyzed. Our study provides insight into the spatiotemporal behavior of phase transitions in crystals of biological molecules and is of general interest to time-resolved crystallographic studies, where the kinetics of conformational changes may be governed by the kinetics of an associated SSPT.
Collapse
Affiliation(s)
- Saminathan Ramakrishnan
- Structural Biophysics Laboratory, Centre for Cancer Research, National Cancer Institute, Frederick, Maryland 21702, USA
| | - Jason R. Stagno
- Structural Biophysics Laboratory, Centre for Cancer Research, National Cancer Institute, Frederick, Maryland 21702, USA
| | - Valentin Magidson
- Optical Microscopy and Analysis Laboratory, Cancer Research Technology Program, Frederick National Laboratory for Cancer Research, Frederick, Maryland 21702, USA
| | - William F. Heinz
- Optical Microscopy and Analysis Laboratory, Cancer Research Technology Program, Frederick National Laboratory for Cancer Research, Frederick, Maryland 21702, USA
| | - Yun-Xing Wang
- Structural Biophysics Laboratory, Centre for Cancer Research, National Cancer Institute, Frederick, Maryland 21702, USA
| |
Collapse
|
16
|
Tani T, Koike-Tani M, Tran MT, Shribak M, Levic S. Postnatal structural development of mammalian Basilar Membrane provides anatomical basis for the maturation of tonotopic maps and frequency tuning. Sci Rep 2021; 11:7581. [PMID: 33828185 PMCID: PMC8027603 DOI: 10.1038/s41598-021-87150-w] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2020] [Accepted: 03/16/2021] [Indexed: 02/01/2023] Open
Abstract
The basilar membrane (BM) of the mammalian cochlea constitutes a spiraling acellular ribbon that is intimately attached to the organ of Corti. Its graded stiffness, increasing from apex to the base of the cochlea provides the mechanical basis for sound frequency analysis. Despite its central role in auditory signal transduction, virtually nothing is known about the BM's structural development. Using polarized light microscopy, the present study characterized the architectural transformations of freshly dissected BM at time points during postnatal development and maturation. The results indicate that the BM structural elements increase progressively in size, becoming radially aligned and more tightly packed with maturation and reach the adult structural signature by postnatal day 20 (P20). The findings provide insight into structural details and developmental changes of the mammalian BM, suggesting that BM is a dynamic structure that changes throughout the life of an animal.
Collapse
Affiliation(s)
- Tomomi Tani
- Marine Biological Laboratory, Eugene Bell Center, Woods Hole, MA, USA
- Biomedical Research Institute, National Institute of Advanced Industrial Science and Technology, Ikeda, Osaka, Japan
| | - Maki Koike-Tani
- Marine Biological Laboratory, Eugene Bell Center, Woods Hole, MA, USA
- Integrated Frontier Research for Medical Science Division, Institute for Open and Transdisciplinary Research Initiatives (OTRI), Osaka University, Suita, Osaka, Japan
| | - Mai Thi Tran
- Marine Biological Laboratory, Eugene Bell Center, Woods Hole, MA, USA
- College of Engineering and Computer Science, VinUniversity, Gia Lam District, Hanoi, Vietnam
| | - Michael Shribak
- Marine Biological Laboratory, Eugene Bell Center, Woods Hole, MA, USA
| | - Snezana Levic
- Marine Biological Laboratory, Eugene Bell Center, Woods Hole, MA, USA.
- Sensory Neuroscience Research Group, School of Pharmacy and Biomolecular Sciences, University of Brighton, Huxley Building, Brighton, BN2 4GJ, UK.
- Brighton and Sussex Medical School, University of Sussex, Brighton, BN1 9PX, UK.
| |
Collapse
|
17
|
Vitkunaite A, Laurinaviciene A, Plancoulaine B, Rasmusson A, Levenson R, Shribak M, Laurinavicius A. Intranuclear birefringent inclusions in paraffin sections by polychromatic polarization microscopy. Sci Rep 2021; 11:6275. [PMID: 33737593 PMCID: PMC7973427 DOI: 10.1038/s41598-021-85667-8] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2020] [Accepted: 03/03/2021] [Indexed: 11/25/2022] Open
Abstract
Intranuclear birefringent inclusions (IBI) found in various cell types in paraffin-embedded tissue sections have long been considered to be a tissue processing artifact, although an association with biological processes has been suggested. We applied polychromatic polarization microscopy to image their spatial organization. Our study provides evidence that IBI are caused by liquid paraffin-macromolecular crystals formed during paraffin-embedding procedures within cells and potentially reflect an active transcriptional status.
Collapse
Affiliation(s)
- Aiste Vitkunaite
- National Center of Pathology, Affiliate of Vilnius University Hospital Santaros Clinics, Vilnius, Lithuania
| | - Aida Laurinaviciene
- National Center of Pathology, Affiliate of Vilnius University Hospital Santaros Clinics, Vilnius, Lithuania.,Institute of Biomedical Sciences, Faculty of Medicine, Vilnius University, Vilnius, Lithuania
| | - Benoit Plancoulaine
- Institute of Biomedical Sciences, Faculty of Medicine, Vilnius University, Vilnius, Lithuania.,ANTICIPE, Inserm (UMR 1086), Cancer Center F. Baclesse, Normandy University, Caen, France
| | - Allan Rasmusson
- National Center of Pathology, Affiliate of Vilnius University Hospital Santaros Clinics, Vilnius, Lithuania.,Institute of Biomedical Sciences, Faculty of Medicine, Vilnius University, Vilnius, Lithuania
| | - Richard Levenson
- Institute of Biomedical Sciences, Faculty of Medicine, Vilnius University, Vilnius, Lithuania.,Department of Pathology and Laboratory Medicine, UC Davis Health, Sacramento, CA, USA
| | - Michael Shribak
- Institute of Biomedical Sciences, Faculty of Medicine, Vilnius University, Vilnius, Lithuania.,Marine Biological Laboratory of University of Chicago, Woods Hole, MA, USA
| | - Arvydas Laurinavicius
- National Center of Pathology, Affiliate of Vilnius University Hospital Santaros Clinics, Vilnius, Lithuania. .,Institute of Biomedical Sciences, Faculty of Medicine, Vilnius University, Vilnius, Lithuania.
| |
Collapse
|
18
|
A Survey of Transposon Landscapes in the Putative Ancient Asexual Ostracod Darwinula stevensoni. Genes (Basel) 2021; 12:genes12030401. [PMID: 33799706 PMCID: PMC7998251 DOI: 10.3390/genes12030401] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2021] [Revised: 03/02/2021] [Accepted: 03/06/2021] [Indexed: 11/17/2022] Open
Abstract
How asexual reproduction shapes transposable element (TE) content and diversity in eukaryotic genomes remains debated. We performed an initial survey of TE load and diversity in the putative ancient asexual ostracod Darwinula stevensoni. We examined long contiguous stretches of DNA in clones from a genomic fosmid library, totaling about 2.5 Mb, and supplemented these data with results on TE abundance and diversity from an Illumina draft genome. In contrast to other TE studies in putatively ancient asexuals, which revealed relatively low TE content, we found that at least 19% of the fosmid dataset and 26% of the genome assembly corresponded to known transposons. We observed a high diversity of transposon families, including LINE, gypsy, PLE, mariner/Tc, hAT, CMC, Sola2, Ginger, Merlin, Harbinger, MITEs and helitrons, with the prevalence of DNA transposons. The predominantly low levels of sequence diversity indicate that many TEs are or have recently been active. In the fosmid data, no correlation was found between telomeric repeats and non-LTR retrotransposons, which are present near telomeres in other taxa. Most TEs in the fosmid data were located outside of introns and almost none were found in exons. We also report an N-terminal Myb/SANT-like DNA-binding domain in site-specific R4/Dong non-LTR retrotransposons. Although initial results on transposable loads need to be verified with high quality draft genomes, this study provides important first insights into TE dynamics in putative ancient asexual ostracods.
Collapse
|
19
|
Yang B, Lee PY, Hua Y, Brazile B, Waxman S, Ji F, Zhu Z, Sigal IA. Instant polarized light microscopy for imaging collagen microarchitecture and dynamics. JOURNAL OF BIOPHOTONICS 2021; 14:e202000326. [PMID: 33103363 PMCID: PMC7887070 DOI: 10.1002/jbio.202000326] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/13/2020] [Revised: 10/17/2020] [Accepted: 10/23/2020] [Indexed: 05/29/2023]
Abstract
Collagen fibers are a primary load-bearing component of connective tissues and are therefore central to tissue biomechanics and pathophysiology. Understanding collagen architecture and behavior under dynamic loading requires a quantitative imaging technique with simultaneously high spatial and temporal resolutions. Suitable techniques are thus rare and often inaccessible. In this study, we present instant polarized light microscopy (IPOL), in which a single snapshot image encodes information on fiber orientation and retardance, thus fulfilling the requirement. We utilized both simulation and experimental data from collagenous tissues of chicken tendon, sheep eye, and porcine heart to evaluate the effectiveness of IPOL as a quantitative imaging technique. We demonstrate that IPOL allows quantitative characterization of micron-scale collagen fiber architecture at full camera frame rates (156 frames/second herein).
Collapse
Affiliation(s)
- Bin Yang
- Department of Ophthalmology, University of Pittsburgh School of Medicine, Pittsburgh, PA, United States
- Department of Engineering, Rangos School of Health Sciences, Duquesne University, Pittsburgh, PA, United States
| | - Po-Yi Lee
- Department of Ophthalmology, University of Pittsburgh School of Medicine, Pittsburgh, PA, United States
- Department of Bioengineering, Swanson School of Engineering, University of Pittsburgh, Pittsburgh, PA, United States
| | - Yi Hua
- Department of Ophthalmology, University of Pittsburgh School of Medicine, Pittsburgh, PA, United States
| | - Bryn Brazile
- Department of Ophthalmology, University of Pittsburgh School of Medicine, Pittsburgh, PA, United States
| | - Susannah Waxman
- Department of Ophthalmology, University of Pittsburgh School of Medicine, Pittsburgh, PA, United States
| | - Fengting Ji
- Department of Ophthalmology, University of Pittsburgh School of Medicine, Pittsburgh, PA, United States
- Department of Bioengineering, Swanson School of Engineering, University of Pittsburgh, Pittsburgh, PA, United States
| | - Ziyi Zhu
- Department of Ophthalmology, University of Pittsburgh School of Medicine, Pittsburgh, PA, United States
- Department of Bioengineering, Swanson School of Engineering, University of Pittsburgh, Pittsburgh, PA, United States
| | - Ian A Sigal
- Department of Ophthalmology, University of Pittsburgh School of Medicine, Pittsburgh, PA, United States
- Department of Bioengineering, Swanson School of Engineering, University of Pittsburgh, Pittsburgh, PA, United States
| |
Collapse
|
20
|
Shoji M, Wakayama T, Ishida H, Kowa H, Sakaue K, Miura T, Higashiguchi T. Single-shot multispectral birefringence mapping by supercontinuum vector beams. APPLIED OPTICS 2020; 59:7131-7138. [PMID: 32788810 DOI: 10.1364/ao.393419] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/24/2020] [Accepted: 07/07/2020] [Indexed: 06/11/2023]
Abstract
We demonstrated a single-shot, multispectral birefringence mapping by use of a supercontinuum (SC) vector beam. The vector beam, which was generated by a pair of axially symmetric wave plates, leads to angular-variant polarization modulation to divide birefringence properties of a sample substrate into Fourier space. This strategy allows multispectral birefringence mapping from a single-shot image captured by a multispectral imaging detector. For SC vector beam analysis, we also compensated the retardance error of the axially symmetric wave plate in the superbroadband spectrum. Resolutions of retardance and azimuthal angle were 0.4° and 0.2°, respectively, and the spatial resolution was 60 µm. Those results are expected to provide us a single-shot, multispectral birefringence mapping with high spatial resolution as compared with using a scanning laser microscope. Our proposal has extendibility to develop high-speed, high-resolution birefringence imaging spectroscopy.
Collapse
|
21
|
Keikhosravi A, Li B, Liu Y, Conklin MW, Loeffler AG, Eliceiri KW. Non-disruptive collagen characterization in clinical histopathology using cross-modality image synthesis. Commun Biol 2020; 3:414. [PMID: 32737412 PMCID: PMC7395097 DOI: 10.1038/s42003-020-01151-5] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2019] [Accepted: 07/16/2020] [Indexed: 12/20/2022] Open
Abstract
The importance of fibrillar collagen topology and organization in disease progression and prognostication in different types of cancer has been characterized extensively in many research studies. These explorations have either used specialized imaging approaches, such as specific stains (e.g., picrosirius red), or advanced and costly imaging modalities (e.g., second harmonic generation imaging (SHG)) that are not currently in the clinical workflow. To facilitate the analysis of stromal biomarkers in clinical workflows, it would be ideal to have technical approaches that can characterize fibrillar collagen on standard H&E stained slides produced during routine diagnostic work. Here, we present a machine learning-based stromal collagen image synthesis algorithm that can be incorporated into existing H&E-based histopathology workflow. Specifically, this solution applies a convolutional neural network (CNN) directly onto clinically standard H&E bright field images to extract information about collagen fiber arrangement and alignment, without requiring additional specialized imaging stains, systems or equipment.
Collapse
Affiliation(s)
- Adib Keikhosravi
- Department of Biomedical Engineering, University of Wisconsin-Madison, Madison, WI, USA
- Laboratory for Optical and Computational Instrumentation, University of Wisconsin-Madison, Madison, WI, USA
| | - Bin Li
- Department of Biomedical Engineering, University of Wisconsin-Madison, Madison, WI, USA
- Laboratory for Optical and Computational Instrumentation, University of Wisconsin-Madison, Madison, WI, USA
- Morgridge Institute for Research, Madison, WI, USA
| | - Yuming Liu
- Laboratory for Optical and Computational Instrumentation, University of Wisconsin-Madison, Madison, WI, USA
| | - Matthew W Conklin
- Department of Cell and Regenerative Biology, University of Wisconsin-Madison, Madison, WI, USA
| | - Agnes G Loeffler
- Department of Pathology, MetroHealth Medical Center, Cleveland, OH, USA
| | - Kevin W Eliceiri
- Department of Biomedical Engineering, University of Wisconsin-Madison, Madison, WI, USA.
- Laboratory for Optical and Computational Instrumentation, University of Wisconsin-Madison, Madison, WI, USA.
- Morgridge Institute for Research, Madison, WI, USA.
- Department of Medical Physics, University of Wisconsin-Madison, Madison, WI, USA.
| |
Collapse
|
22
|
Abstract
The premise of this book is the importance of the tumor microenvironment (TME). Until recently, most research on and clinical attention to cancer biology, diagnosis, and prognosis were focused on the malignant (or premalignant) cellular compartment that could be readily appreciated using standard morphology-based imaging.
Collapse
|
23
|
Fereidouni F, Todd A, Li Y, Chang CW, Luong K, Rosenberg A, Lee YJ, Chan JW, Borowsky A, Matsukuma K, Jen KY, Levenson R. Dual-mode emission and transmission microscopy for virtual histochemistry using hematoxylin- and eosin-stained tissue sections. BIOMEDICAL OPTICS EXPRESS 2019; 10:6516-6530. [PMID: 31853414 PMCID: PMC6913420 DOI: 10.1364/boe.10.006516] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/04/2019] [Revised: 11/18/2019] [Accepted: 11/19/2019] [Indexed: 05/23/2023]
Abstract
In the clinical practice of pathology, trichrome stains are commonly used to highlight collagen and to help evaluate fibrosis. Such stains do delineate collagen deposits but are not molecularly specific and can suffer from staining inconsistencies. Moreover, performing histochemical stain evaluation requires the preparation of additional sections beyond the original hematoxylin- and eosin-stained slides, as well as additional staining steps, which together add cost, time, and workflow complications. We have developed a new microscopy approach, termed DUET (DUal-mode Emission and Transmission) that can be used to extract signals that would typically require special stains or advanced optical methods. Our preliminary analysis demonstrates the potential of using the resulting signals to generate virtual histochemical images that resemble trichrome-stained slides and can support clinical evaluation. We demonstrate advantages of this approach over images acquired from conventional trichrome-stained slides and compare them with images created using second harmonic generation microscopy.
Collapse
Affiliation(s)
- Farzad Fereidouni
- Department of Pathology and Laboratory Medicine, UC Davis Health, 4400 V Street, Sacramento, CA 95817, USA
| | - Austin Todd
- Department of Pathology and Laboratory Medicine, UC Davis Health, 4400 V Street, Sacramento, CA 95817, USA
| | - Yuheng Li
- Department of Computer Science, UC Davis, One Shields Avenue, Davis, CA 95616, USA
| | - Che-Wei Chang
- Department of Pathology and Laboratory Medicine, UC Davis Health, 4400 V Street, Sacramento, CA 95817, USA
| | - Keith Luong
- Department of Electrical and Computer Engineering, UC Davis, One Shields Avenue, Davis, CA 95616, USA
| | - Avi Rosenberg
- Renal Pathology, Department of Pathology, Johns Hopkins University and Johns Hopkins Hospital, Baltimore, MD 21287, USA
| | - Yong-Jae Lee
- Department of Computer Science, UC Davis, One Shields Avenue, Davis, CA 95616, USA
| | - James W. Chan
- Department of Pathology and Laboratory Medicine, UC Davis Health, 4400 V Street, Sacramento, CA 95817, USA
| | - Alexander Borowsky
- Department of Pathology and Laboratory Medicine, UC Davis Health, 4400 V Street, Sacramento, CA 95817, USA
| | - Karen Matsukuma
- Department of Pathology and Laboratory Medicine, UC Davis Health, 4400 V Street, Sacramento, CA 95817, USA
| | - Kuang-Yu Jen
- Department of Pathology and Laboratory Medicine, UC Davis Health, 4400 V Street, Sacramento, CA 95817, USA
| | - Richard Levenson
- Department of Pathology and Laboratory Medicine, UC Davis Health, 4400 V Street, Sacramento, CA 95817, USA
| |
Collapse
|
24
|
Li X, Liao R, Zhou J, Leung PTY, Yan M, Ma H. Classification of morphologically similar algae and cyanobacteria using Mueller matrix imaging and convolutional neural networks. APPLIED OPTICS 2017; 56:6520-6530. [PMID: 29047942 DOI: 10.1364/ao.56.006520] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/02/2023]
Abstract
We present the Mueller matrix imaging system to classify morphologically similar algae based on convolutional neural networks (CNNs). The algae and cyanobacteria data set contains 10,463 Mueller matrices from eight species of algae and one species of cyanobacteria, belonging to four phyla, the shapes of which are mostly randomly oriented spheres, ovals, wheels, or rods. The CNN serves as an automatic machine with learning ability to help in extracting features from the Mueller matrix, and trains a classifier to achieve a 97% classification accuracy. We compare the performance in two ways. One way is to compare the performance of five CNNs that differ in the number of convolution layers as well as the classical principle component analysis (PCA) plus the support vector machine (SVM) method; the other way is to quantify the differences of scores between full Mueller matrix and the first matrix element m11, which does not contain polarization information under the same conditions. As the results show, deeper CNNs perform better, the best of which outperforms the conventional PCA plus SVM method by 19.66% in accuracy, and using the full Mueller matrix earns 6.56% increase of accuracy than using m11. It demonstrates that the coupling of Mueller matrix imaging and CNN may be a promising and efficient solution for the automatic classification of morphologically similar algae.
Collapse
|
25
|
Harmany ZT, Fereidouni F, Levenson RM. Spectral Unmixing Methods and Tools for the Detection and Quantitation of Collagen and Other Macromolecules in Tissue Specimens. Methods Mol Biol 2017; 1627:491-509. [PMID: 28836220 DOI: 10.1007/978-1-4939-7113-8_30] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
Collagen and other components in the extracellular matrix are proving of increasing importance for the understanding of complex cell and tissue interactions in a variety of settings. Detection and quantitation of these components can still prove challenging, and a number of techniques have been developed. We focus here on methods in fluorescence-based assessments, including multiplexed immunodetection and the use of simpler histochemical stains, both complemented by linear unmixing techniques. Typically, differentiating these components requires the use of a set of optical filters to isolate each fluorescent compound from each other and from often bright background autofluorescence signals. However, standard fluorescent microscopes are usually only able to separate a limited number of components. If the emission spectra of the fluorophores are spectrally distinct, but overlapping, sophisticated spectral imaging or computational methods can be used to optimize separation and quantitation. This chapter describes spectral unmixing methodology and associated open-source software tools available to analyze multispectral as well as simple color (RGB) images.
Collapse
Affiliation(s)
- Zachary T Harmany
- Department of Pathology and Laboratory Medicine, University of California-Davis Medical Center, Sacramento, CA, USA.
| | - Farzad Fereidouni
- Department of Pathology and Laboratory Medicine, University of California-Davis Medical Center, Sacramento, CA, USA
| | - Richard M Levenson
- Department of Pathology and Laboratory Medicine, University of California-Davis Medical Center, Sacramento, CA, USA
| |
Collapse
|
26
|
Tani T, Shribak M, Oldenbourg R. Living Cells and Dynamic Molecules Observed with the Polarized Light Microscope: the Legacy of Shinya Inoué. THE BIOLOGICAL BULLETIN 2016; 231:85-95. [PMID: 27638697 PMCID: PMC5319827 DOI: 10.1086/689593] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
Abstract
In 1948, Shinya Inoué arrived in the United States for graduate studies at Princeton. A year later he came to Woods Hole, starting a long tradition of summer research at the Marine Biological Laboratory (MBL), which quickly became Inoué's scientific home. Primed by his Japanese mentor, Katsuma Dan, Inoué followed Dan's mantra to work with healthy, living cells, on a fundamental problem (mitosis), with a unique tool set that he refined for precise and quantitative observations (polarized light microscopy), and a fresh and brilliant mind that was unafraid of challenging current dogma. Building on this potent combination, Inoué contributed landmark observations and concepts in cell biology, including the notion that there are dynamic, fine structures inside living cells, in which molecular assemblies such as mitotic spindle fibers exist in delicate equilibrium with their molecular building blocks suspended in the cytoplasm. In the late 1970s and 1980s, Inoué and others at the MBL were instrumental in conceiving video microscopy, a groundbreaking technique which married light microscopy and electronic imaging, ushering in a revolution in how we know and what we know about living cells and the molecular mechanisms of life. Here, we recount some of Inoué's accomplishments and describe how his legacy has shaped current activities in polarized light imaging at the MBL.
Collapse
Affiliation(s)
- Tomomi Tani
- Marine Biological Laboratory, Woods Hole, Massachusetts 02543
| | - Michael Shribak
- Marine Biological Laboratory, Woods Hole, Massachusetts 02543
| | | |
Collapse
|